PhyloFacts Plasmodium Library

PhyloFacts v. 2.0. 24 November 2009

The PhyloFacts Plasmodium Library focuses on the proteins and protein domains of the human malarial pathogen Plasmodium falciparum. Of the four types of human malarial infection, P. falciparum is by far the most deadly.

Protein Search

Submit sequences for classification against the HMM library. This library is designed to help biologists do the following:

• Predict molecular function by phylogenomic analysis, using the phylogenetic tree for the family.
• Classify novel sequences to functional subtypes, using the subfamily HMMs for the family.
• Predict specificity positions, using the alignment analysis plots for each family.

Each "book" in the HMM library corresponds to a structural domain, and contains the following data (generally downloadable, in different formats):

• A cluster of homologs, typically from many species
• One or more phylogenetic trees.
• A decomposition of the tree into subtrees, to identify functional subfamilies.
• A multiple sequence alignment for the family, as well as for individual subfamilies.
• GO (Gene Ontology) annotations and evidence codes.
• Other annotations and experimental data.
• Hyperlinks to papers and online resources.
• An analysis of the family's multiple sequence alignment using the subfamily decomposition to predict specificity positions defining the individual subtypes.
• One or more solved structures, overlaid with subfamily-specific and family-wide conservation patterns for prediction of active site and other specificity positions .